A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.
Report
generated on 2022-09-28, 19:38
based on data in:
/home/qinchunyuan/proteomicsDIA/mzml/pmultiqc_test
pmultiqc
pmultiqc is a multiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms.
Experimental Design
This table shows the design of the experiment. I.e., which files and channels correspond to which sample/condition/fraction.
You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html
| Spectra File | Fraction_Group | Fraction | Label | Sample | MSstats_Condition | MSstats_BioReplicate |
|---|---|---|---|---|---|---|
| SWATH-TN-10-1.wiff.mzML | 3 | 1 | 1 | 2 | breast cancer | 2 |
| SWATH-TN-10-2.wiff.mzML | 4 | 1 | 1 | 2 | breast cancer | 2 |
| SWATH-TN-9-1.wiff.mzML | 1 | 1 | 1 | 1 | breast cancer | 1 |
| SWATH-TN-9-2.wiff.mzML | 2 | 1 | 1 | 1 | breast cancer | 1 |
Summary Table
This table shows the quantms pipeline summary statistics
This table shows the quantms pipeline summary statistics
| #MS2 Spectra | #Peptides Quantified | #Proteins Quantified |
|---|---|---|
| 534120 | 19163 | 3629 |
Pipeline Result Statistics
This plot shows the quantms pipeline final result
This plot shows the quantms pipeline final result.
Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、
and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained
from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.
| Spectra File | Sample Name | Condition | Fraction | #Peptide IDs | #Unambiguous Peptide IDs | #Modified Peptide IDs | #Protein (group) IDs |
|---|---|---|---|---|---|---|---|
| SWATH-TN-10-1.wiff.mzML | 2 | breast cancer | 1 | 9270 | 9270 | 0 | 3379 |
| SWATH-TN-10-2.wiff.mzML | 2 | breast cancer | 1 | 11046 | 11046 | 0 | 3706 |
| SWATH-TN-9-1.wiff.mzML | 1 | breast cancer | 1 | 12771 | 12771 | 0 | 3952 |
| SWATH-TN-9-2.wiff.mzML | 1 | breast cancer | 1 | 14471 | 14471 | 0 | 4440 |
Number of Peptides Per Protein
This plot shows the number of peptides per proteins in quantms pipeline final result
This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.
Distribution of precursor charges
This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.
This information can be used to identify potential ionization problems including many 1+ charges from an ESI ionization source or an unexpected distribution of charges. MALDI experiments are expected to contain almost exclusively 1+ charged ions. An unexpected charge distribution may furthermore be caused by specific search engine parameter settings such as limiting the search to specific ion charges.
Number of Peaks per MS/MS spectrum
This chart represents a histogram containing the number of peaks per MS/MS spectrum in a given experiment. This chart assumes centroid data. Too few peaks can identify poor fragmentation or a detector fault, as opposed to a large number of peaks representing very noisy spectra. This chart is extensively dependent on the pre-processing steps performed to the spectra (centroiding, deconvolution, peak picking approach, etc).
Peak Intensity Distribution
This is a histogram representing the ion intensity vs. the frequency for all MS2 spectra in a whole given experiment. It is possible to filter the information for all, identified and unidentified spectra. This plot can give a general estimation of the noise level of the spectra.
Generally, one should expect to have a high number of low intensity noise peaks with a low number of high intensity signal peaks. A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or potential experimental problems. In the case of data reuse this plot can be useful in identifying the requirement for pre-processing of the spectra prior to any downstream analysis. The quality of the identifications is not linked to this data as most search engines perform internal spectrum pre-processing before matching the spectra. Thus, the spectra reported are not necessarily pre-processed since the search engine may have applied the pre-processing step internally. This pre-processing is not necessarily reported in the experimental metadata.
nf-core/quantms Software Versions
are collected at run time from the software output.
| Process Name | Software | Version |
|---|---|---|
| ASSEMBLE_EMPIRICAL_LIBRARY | DIA-NN | 1.8.1 |
| CUSTOM_DUMPSOFTWAREVERSIONS | python | 3.9.5 |
| yaml | 5.4.1 | |
| DIANNCFG | sdrf-pipelines | 0.0.21 |
| DIANNCONVERT | pmultiqc | 0.0.13 |
| DIANN_PRELIMINARY_ANALYSIS | DIA-NN | 1.8.1 |
| INDIVIDUAL_FINAL_ANALYSIS | DIA-NN | 1.8.1 |
| MZMLINDEXING | FileConverter | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| SAMPLESHEET_CHECK | sdrf-pipelines | 0.0.21 |
| SDRFPARSING | sdrf-pipelines | 0.0.21 |
| Workflow | Nextflow | 21.10.6 |
| nf-core/quantms | 1.1dev |
nf-core/quantms Workflow Summary
- this information is collected when the pipeline is started.
Core Nextflow options
- runName
- friendly_edison
- containerEngine
- singularity
- launchDir
- /hps/nobackup/juan/pride/reanalysis/dia-projects/PXD014194
- workDir
- /hps/nobackup/juan/pride/reanalysis/dia-projects/PXD014194/work
- projectDir
- /hps/nobackup/juan/pride/reanalysis/quantms
- userName
- pst_prd
- profile
- ebiclusters
- configFiles
- /hps/nobackup/juan/pride/reanalysis/quantms/nextflow.config, /hps/nobackup/juan/pride/reanalysis/quantms/nextflow.config
Input/output options
- input
- PXD014194.sdrf.tsv
- outdir
- PXD014194
- yperez@ebi.ac.uk
- root_folder
- /hps/nobackup/juan/pride/reanalysis/dia-projects/PXD014194/
Protein database
- database
- /hps/nobackup/juan/pride/reanalysis/multiomics-configs/databases/Homo-sapiens-uniprot-reviewed-isoforms-contaminants-202105.fasta
Database search
- allowed_missed_cleavages
- 1
- instrument
- N/A
- max_mods
- 1
Modification localization
- luciphor_debug
- N/A
PSM re-scoring (general)
- run_fdr_cutoff
- 0.10
PSM re-scoring (Percolator)
- description_correct_features
- N/A
Consensus ID
- consensusid_considered_top_hits
- N/A
- min_consensus_support
- 1
Isobaric analyzer
- select_activation
- HCD
Protein Quantification (DDA)
- ratios
- N/A
- normalize
- N/A
- fix_peptides
- N/A
DIA-NN
- acquisition_method
- N/A
- mass_acc_ms2
- 13
- mass_acc_ms1
- 7
- scan_window
- 8
Statistical post-processing
- skip_post_msstats
- true
- contrasts
- pairwise
Quality control
- enable_pmultiqc
- true
Max job request options
- max_cpus
- 48
- max_memory
- 300 GB
- max_time
- 10d
Generic options
- email_on_fail
- yperez@ebi.ac.uk
- hostnames
- N/A